Pedosphere 30(1): 87--97, 2020
ISSN 1002-0160/CN 32-1315/P
©2020 Soil Science Society of China
Published by Elsevier B.V. and Science Press
Evidence for niche differentiation of nitrifying communities in grassland soils after 44 years of different field fertilization scenarios
Zhongjun JIA1, Xue ZHOU2, Weiwei XIA1,3, Dario FORNARA4, Baozhan WANG1, Elizabeth Anne WASSON4, Peter CHRISTIE4, Martin F. POLZ5, David D. MYROLD6
1State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008(China)
2State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098(China)
3Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044(China)
4Agri-Food and Biosciences Institute, Belfast BT9 5PX(UK)
5Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge MA 02139(USA)
6Department of Crop and Soil Science, Oregon State University, Corvallis OR 97331(USA)
Corresponding Author:Zhongjun JIA
      Long-term nitrogen (N) fertilization imposes strong selection on nitrifying communities in agricultural soil, but how a progressively changing niche affects potentially active nitrifiers in the field remains poorly understood. Using a 44-year grassland fertilization experiment, we investigated community shifts of active nitrifiers by DNA-based stable isotope probing (SIP) of field soils that received no fertilization (CK), high levels of organic cattle manure (HC), and chemical N fertilization (CF). Incubation of DNA-SIP microcosms showed significant nitrification activities in CF and HC soils, whereas no activity occurred in CK soils. The 44 years of inorganic N fertilization selected only 13C-ammonia-oxidizing bacteria (AOB), whereas cattle slurry applications created a niche in which both ammonia-oxidizing archaea (AOA) and AOB could be actively 13C-labeled. Phylogenetic analysis indicated that Nitrosospira sp. 62-like AOB dominated inorganically fertilized CF soils, while Nitrosospira sp. 41-like AOB were abundant in organically fertilized HC soils. The 13C-AOA in HC soils were affiliated with the 29i4 lineage. The 13C-nitrite-oxidizing bacteria (NOB) were dominated by both Nitrospira-and Nitrobacter-like communities in CF soils, and the latter was overwhelmingly abundant in HC soils. The 13C-labeled nitrifying communities in SIP microcosms of CF and HC soils were largely similar to those predominant under field conditions. These results provide direct evidence for a strong selection of distinctly active nitrifiers after 44 years of different fertilization regimes in the field. Our findings imply that niche differentiation of nitrifying communities could be assessed as a net result of microbial adaption over 44 years to inorganic and organic N fertilization in the field, where distinct nitrifiers have been shaped by intensified anthropogenic N input.
Key Words:  ammonia-oxidizing archaea,ammonia-oxidizing bacteria,community shift,long-term fertilization,nitrite-oxidizing bacteria,nitrogen enrichment,stable isotope probing microcosm
Citation: Jia Z J, Zhou X, Xia W W, Fornara D, Wang B Z, Wasson E A, Christie P, Polz M F, Myrold D D. 2020. Evidence for niche differentiation of nitrifying communities in grassland soils after 44 years of different field fertilization scenarios. Pedosphere. 30(1):87-97.
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